A modular view of the bacteriophage genomic space: Identification of host and lifestyle marker modules

Research in Microbiology

Volumn 162, Issue 8, 2011, Pages 737-746

  Lima Mendez, Gipsi ^a   Toussaint, Ariane ^b   Leplae, Raphael ^b  

^a VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Bacteriophage; Functional module; Phage classification; Phage evolution; Prophage; Transposable phage

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIOPHAGE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROPHAGE;

BACTERIA; BACTERIOPHAGES; GENOME, VIRAL; HOST SPECIFICITY; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROPHAGES; VIRAL PROTEINS;

BACTERIA (MICROORGANISMS);

EID: 80053386018     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2011.06.006     Document Type: Article

References (29)

1. Abbes C., Joseleau-Petit D., Liebart J.C., D'Ari R., Sezonov G. The GemA protein of phage Mu and the GyrB gyrase subunit of Escherichia coli: the search for targets and interactions leading to the reversion of Mu-induced mutations. Biochimie 2001, 83:261-267.
2. Abdi H. Bonferroni and Sidak corrections for multiple comparisons. Encyclopedia of Measurement and Statistics 2007, 103-107. Sage, Thousand Oaks (CA). N.J. Salkind (Ed.).
3. Botstein D. A theory of modular evolution for bacteriophages. Ann N Y Acad Sci. 1980, 484-490.
4. Cunningham J.T., Bruno S.B., Higgs K.A., Sullivan M.J. Intrapericardial procaine affects volume expansion-induced fos immunoreactivity in unanesthetized rats. Exp. Neurol. 2002, 174:181-192.
5. Fouts D.E., Mongodin E.F., Mandrell R.E., Miller W.G., Rasko D.A., Ravel J., Brinkac L.M., DeBoy R.T., et al. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol. 2005, 3:e15.
6. Hatfull G.F., Pedulla M.L., Jacobs-Sera D., Cichon P.M., Foley A., Ford M.E., Gonda R.M., Houtz J.M., et al. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2006, 2:e92.
7. Hendrix R.W. Bacteriophage genomics. Curr. Opin. Microbiol. 2003, 6:506-511.
8. Hendrix R.W., Smith M.C., Burns R.N., Ford M.E., Hatfull G.F. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 1999, 2192-2197.
9. Juhala R.J., Ford M.E., Duda R.L., Youlton A., Hatfull G.F., Hendrix R.W. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 2000, 299:27-51.
10. Klee S.R., Nassif X., Kusecek B., Merker P., Beretti J.L., Achtman M., Tinsley C.R. Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae. Infect. Immun. 2000, 68:2082-2095.
11. Labrie S., Moineau S. Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. Virology 2002, 296:308-320.
12. Lavigne R., Darius P., Summer E.J., Seto D., Mahadevan P., Nilsson A.S., Ackermann H.W., Kropinski A.M. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 2009, 9:224.
13. Lavigne R., Seto D., Mahadevan P., Ackermann H.-W., Kropinski A.M. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res. Microbiol 2008, 406-414.
14. Lawrence J., Hatfull G., Hendrix R. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 2002, 4891-4905.
15. Leplae R., Lima-Mendez G., Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. 2010, 38:D57-D61.
16. Lima-Mendez G., Toussaint A., Leplae R. Analysis of the phage sequence space: the benefit of structured information. Virology 2007, 241-249.
17. Lima-Mendez G., van Helden J., Toussaint A., Leplae R. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 2008, 863-865.
18. Lima-Mendez G., van Helden J., Toussaint A., Leplae R. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol 2008, 762-777.
19. Masignani V., Giuliani M.M., Tettelin H., Comanducci M., Rappuoli R., Scarlato V. Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens. Infect. Immun. 2001, 69:2580-2588.
20. Mikkonen M., Dupont L., Alatossava T., Ritzenthaler P. Defective site-specific integration elements are present in the genome of virulent bacteriophage LL-H of Lactobacillus delbrueckii. Appl. Environ. Microbiol. 1996, 62:1847-1851.
21. Nelson D. Phage taxonomy: we agree to disagree. J. Bacteriol 2004, 7029-7031.
22. Parker C.T., Quinones B., Miller W.G., Horn S.T., Mandrell R.E. Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J. Clin. Microbiol. 2006, 44:4125-4135.
23. Pellegrini M., Marcotte E., Thompson M., Eisenberg D., Yeates T. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 1999, 4285-4288.
24. Petrov V.M., Ratnayaka S., Nolan J.M., Miller E.S., Karam J.D. Genomes of the T4-related bacteriophages as windows on microbial genome evolution. Virol. J. 2010, 7:292.
25. Rohwer F., Edwards R. The Phage Proteomic Tree: a genome-based taxonomy for phage. J. Bacteriol 2002, 4529-4535.
26. Scott A.E., Timms A.R., Connerton P.L., Loc Carrillo C., Adzfa Radzum K., Connerton I.F. Genome dynamics of Campylobacter jejuni in response to bacteriophage predation. PLoS Pathog. 2007, 3:e119.
27. Symonds N., Toussaint A., van de Putte P., Howe M.M. Phage Mu 1987, New York.
28. Toussaint A., Lima-Mendez G., Leplae R. PhiGO, a phage ontology associated with the ACLAME database. Res. Microbiol. 2007, 158:567-571.
29. Tuohimaa A., Riipinen K.A., Brandt K., Alatossava T. The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages. Arch. Virol. 2006, 151:947-965.